Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 2 of 172
Found at i:337119 original size:39 final size:39
Alignment explanation
Indices: 337009--337143 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 39
336999 GACCTCGAGT
* * * *
337009 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** * ** * *
337050 CGATGAGGTAGTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
337088 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
337127 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
337144 CCATATTGGT
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
38 17 0.24
39 35 0.49
40 4 0.06
41 15 0.21
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:337287 original size:18 final size:19
Alignment explanation
Indices: 337266--337306 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
337256 AATGAAATGA
337266 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
337284 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
337303 GAAA
1 GAAA
337307 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:338645 original size:5 final size:5
Alignment explanation
Indices: 338633--338685 Score: 99
Period size: 5 Copynumber: 10.8 Consensus size: 5
338623 AAAAGTTAAG
338633 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
338682 TATA
1 TATA
338686 AAACAAAGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.08
5 44 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:339257 original size:22 final size:22
Alignment explanation
Indices: 339224--339288 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
339214 CGATTACTAA
339224 CACATTAGTGCTCTCTGTTTAG
1 CACATTAGTGCTCTCTGTTTAG
** * *
339246 CACATTCTTGCTTTCTGTATAG
1 CACATTAGTGCTCTCTGTTTAG
*
339268 CACTTTAGTGCTCTCTGTTTA
1 CACATTAGTGCTCTCTGTTTA
339289 ATAGTGCATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (22 bp):
CACATTAGTGCTCTCTGTTTAG
Found at i:340620 original size:13 final size:13
Alignment explanation
Indices: 340604--340628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
340594 CGATCTCTTC
340604 TGGGTATTCTATG
1 TGGGTATTCTATG
340617 TGGGTATTCTAT
1 TGGGTATTCTAT
340629 ATGTTGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.28, T:0.48
Consensus pattern (13 bp):
TGGGTATTCTATG
Found at i:344831 original size:6 final size:5
Alignment explanation
Indices: 344801--344894 Score: 79
Period size: 6 Copynumber: 18.0 Consensus size: 5
344791 ATATGTCTTT
*
344801 TAAAA TAAAA T--AA TAAAA TTGAAA TGAAAA TAAAAA TCAAAA TAAAAA
1 TAAAA TAAAA TAAAA TAAAA -TAAAA T-AAAA T-AAAA T-AAAA T-AAAA
344849 TAAAAA TAAAA TAAAA -AAAA TAAAA TAAAAA TAAGAA T-AAA TAAAA
1 T-AAAA TAAAA TAAAA TAAAA TAAAA T-AAAA TAA-AA TAAAA TAAAA
344895 AAATTGGAGG
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
3 3 0.04
4 7 0.09
5 29 0.38
6 37 0.49
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:344860 original size:49 final size:47
Alignment explanation
Indices: 344802--344895 Score: 125
Period size: 49 Copynumber: 2.0 Consensus size: 47
344792 TATGTCTTTT
* * * *
344802 AAAATAAAATAATAAAATTGAAATGAAAATAAAAATCAAAATAAAAATA
1 AAAATAAAATAAAAAAAATAAAATAAAAATAAAAAT--AAATAAAAATA
*
344851 AAAATAAAATAAAAAAAATAAAATAAAAATAAGAATAAATAAAAA
1 AAAATAAAATAAAAAAAATAAAATAAAAATAAAAATAAATAAAAA
344896 AATTGGAGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 9 0.22
49 31 0.77
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (47 bp):
AAAATAAAATAAAAAAAATAAAATAAAAATAAAAATAAATAAAAATA
Found at i:344867 original size:31 final size:30
Alignment explanation
Indices: 344832--344897 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 30
344822 AAATGAAAAT
344832 AAAAATCAAAATAAAAATAAAAATAAAATAAA
1 AAAAAT-AAAATAAAAATAAAAAT-AAATAAA
*
344864 AAAAATAAAATAAAAATAAGAATAAATAAA
1 AAAAATAAAATAAAAATAAAAATAAATAAA
344894 AAAA
1 AAAA
344898 TTGGAGGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 11 0.33
31 16 0.48
32 6 0.18
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.15
Consensus pattern (30 bp):
AAAAATAAAATAAAAATAAAAATAAATAAA
Found at i:344879 original size:26 final size:27
Alignment explanation
Indices: 344834--344895 Score: 92
Period size: 25 Copynumber: 2.3 Consensus size: 27
344824 ATGAAAATAA
*
344834 AAATCAAAATAAAAATAAAAATAA-AAT
1 AAATAAAAAT-AAAATAAAAATAAGAAT
344861 AAA-AAAAATAAAATAAAAATAAGAAT
1 AAATAAAAATAAAATAAAAATAAGAAT
344887 AAATAAAAA
1 AAATAAAAA
344896 AATTGGAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 13 0.41
26 11 0.34
27 8 0.25
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.16
Consensus pattern (27 bp):
AAATAAAAATAAAATAAAAATAAGAAT
Found at i:352949 original size:11 final size:11
Alignment explanation
Indices: 352891--352986 Score: 84
Period size: 11 Copynumber: 8.7 Consensus size: 11
352881 GTGATGCTAT
*
352891 TTTTTGTGCTG
1 TTTTGGTGCTG
*
352902 TTTGGGTGCTG
1 TTTTGGTGCTG
*
352913 TTTTGTTGCTG
1 TTTTGGTGCTG
* *
352924 TTTGGGTGCTA
1 TTTTGGTGCTG
352935 TTTTGGTGCTG
1 TTTTGGTGCTG
* * *
352946 TTTTGATGGTA
1 TTTTGGTGCTG
352957 TTTTGGTGCTG
1 TTTTGGTGCTG
* * * *
352968 CTTTGATGGTA
1 TTTTGGTGCTG
352979 TTTTGGTG
1 TTTTGGTG
352987 TTATTTTGCT
Statistics
Matches: 64, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 64 1.00
ACGTcount: A:0.05, C:0.07, G:0.33, T:0.54
Consensus pattern (11 bp):
TTTTGGTGCTG
Found at i:352965 original size:33 final size:33
Alignment explanation
Indices: 352867--352966 Score: 101
Period size: 33 Copynumber: 3.0 Consensus size: 33
352857 TTTTGCAGGT
* * * *
352867 TTTTGGTGTTGTTGGTGATGCTATTTTTTGTGCTG
1 TTTTGGTGCTGTT-TTGATGCTA-TTTTGGTGCTA
* * * *
352902 TTTGGGTGCTGTTTTGTTGCTGTTTGGGTGCTA
1 TTTTGGTGCTGTTTTGATGCTATTTTGGTGCTA
*
352935 TTTTGGTGCTGTTTTGATGGTATTTTGGTGCT
1 TTTTGGTGCTGTTTTGATGCTATTTTGGTGCT
352967 GCTTTGATGG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 35 0.67
34 6 0.12
35 11 0.21
ACGTcount: A:0.05, C:0.07, G:0.33, T:0.55
Consensus pattern (33 bp):
TTTTGGTGCTGTTTTGATGCTATTTTGGTGCTA
Found at i:352991 original size:11 final size:11
Alignment explanation
Indices: 352885--353005 Score: 80
Period size: 11 Copynumber: 10.8 Consensus size: 11
352875 TTGTTGGTGA
*
352885 TGCTATTTTTTG
1 TGCTA-TTTTGG
* *
352897 TGCTGTTTGGG
1 TGCTATTTTGG
* *
352908 TGCTGTTTTGT
1 TGCTATTTTGG
* *
352919 TGCTGTTTGGG
1 TGCTATTTTGG
352930 TGCTATTTTGG
1 TGCTATTTTGG
* *
352941 TGCTGTTTTGA
1 TGCTATTTTGG
*
352952 TGGTATTTTGG
1 TGCTATTTTGG
** *
352963 TGCTGCTTTGA
1 TGCTATTTTGG
*
352974 TGGTATTTTGG
1 TGCTATTTTGG
* *
352985 TGTTATTTTGC
1 TGCTATTTTGG
352996 TGCTACTTTT
1 TGCTA-TTTT
353006 TTCCGTGTTT
Statistics
Matches: 83, Mismatches: 25, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
11 75 0.90
12 8 0.10
ACGTcount: A:0.07, C:0.09, G:0.29, T:0.55
Consensus pattern (11 bp):
TGCTATTTTGG
Found at i:352994 original size:22 final size:22
Alignment explanation
Indices: 352867--352986 Score: 105
Period size: 22 Copynumber: 5.4 Consensus size: 22
352857 TTTTGCAGGT
* * *
352867 TTTTGGTGTTGTTGGTGATGCTA
1 TTTTGGTGCTGTT-TTGATGGTA
* * * * *
352890 TTTTTTGTGCTGTTTGGGTGCTG
1 -TTTTGGTGCTGTTTTGATGGTA
* * * *
352913 TTTTGTTGCTGTTTGGGTGCTA
1 TTTTGGTGCTGTTTTGATGGTA
352935 TTTTGGTGCTGTTTTGATGGTA
1 TTTTGGTGCTGTTTTGATGGTA
*
352957 TTTTGGTGCTGCTTTGATGGTA
1 TTTTGGTGCTGTTTTGATGGTA
352979 TTTTGGTG
1 TTTTGGTG
352987 TTATTTTGCT
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
22 66 0.80
23 5 0.06
24 11 0.13
ACGTcount: A:0.06, C:0.07, G:0.33, T:0.54
Consensus pattern (22 bp):
TTTTGGTGCTGTTTTGATGGTA
Found at i:355349 original size:17 final size:18
Alignment explanation
Indices: 355327--355362 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
355317 GATATGATAC
*
355327 TAAAAT-TATTAAAAAAA
1 TAAAATATAATAAAAAAA
355344 TAAAATATAATAAAAAAA
1 TAAAATATAATAAAAAAA
355362 T
1 T
355363 CAGGGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAATATAATAAAAAAA
Found at i:355667 original size:17 final size:18
Alignment explanation
Indices: 355645--355723 Score: 69
Period size: 17 Copynumber: 4.5 Consensus size: 18
355635 ATTACAAAAT
355645 CATATC-TTCTAAGATTG
1 CATATCATTCTAAGATTG
*
355662 CATATCATTTTTAAGATTG
1 CATATCA-TTCTAAGATTG
* *
355681 CA-ATCATATCTGAGAATG
1 CATATCAT-TCTAAGATTG
355699 --TATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTG
355716 CA-ATCATT
1 CATATCATT
355724 GAAGATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 22 0.44
18 16 0.32
19 12 0.24
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (18 bp):
CATATCATTCTAAGATTG
Found at i:356130 original size:45 final size:45
Alignment explanation
Indices: 356073--356272 Score: 240
Period size: 45 Copynumber: 4.5 Consensus size: 45
356063 GGAATGAGAT
* * *
356073 ATCTGCTATCTTTGATCTGCTCCCTGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
356118 ATTTGTTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * *
356163 ATCTGCT-TCTTCAATCTGCACCCTGTCTAATATAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
356207 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGACAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
356252 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
356273 TCGATGTAAA
Statistics
Matches: 131, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
44 37 0.28
45 94 0.72
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:356200 original size:89 final size:90
Alignment explanation
Indices: 356073--356256 Score: 262
Period size: 89 Copynumber: 2.1 Consensus size: 90
356063 GGAATGAGAT
** * * **
356073 ATCTGCTATCTTTGATCTGCTCCCTGTCTAATACAGAGACGCCAAATTTGTTATCTTTGATCTGC
1 ATCTGCTATCTTCAATCTGCACCCTGTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTGC
*
356138 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGACAA
* * *
356163 ATCTGCT-TCTTCAATCTGCACCCTGTCTAATATAGAGATGCCAAATCTGTTATCTCCGATTTGC
1 ATCTGCTATCTTCAATCTGCACCCTGTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTGC
*
356227 TCCCCGTCTAATACAGAGATGACAA
66 TCCCCGTCTAATACAGAGACGACAA
356252 ATCTG
1 ATCTG
356257 TCATCTTGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 76 0.92
90 7 0.08
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCACCCTGTCTAATACAGAGACGCCAAATCTGTTATCTCCGATCTGC
TCCCCGTCTAATACAGAGACGACAA
Found at i:356479 original size:77 final size:78
Alignment explanation
Indices: 356289--356578 Score: 431
Period size: 78 Copynumber: 3.7 Consensus size: 78
356279 TAAACACATT
* * * *
356289 AAGGTCAAATCTGCTATGTCTTCGATCTGCTCCCCTTCAAATACATAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
356354 ATCTGCTTCAATG
66 ATCTGCTTCAATG
* * *
356367 AAGGTCCA-ATTTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATACCAAATCATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
*
356431 GATCT-ATTCAATG
65 GATCTGCTTCAATG
*
356444 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
356509 ATCTGCTTCAATA
66 ATCTGCTTCAATG
* * **
356522 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAAT
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAAT
356579 ATGTTTCTTC
Statistics
Matches: 191, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
76 2 0.01
77 69 0.36
78 118 0.62
79 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:356571 original size:155 final size:155
Alignment explanation
Indices: 356289--356578 Score: 447
Period size: 155 Copynumber: 1.9 Consensus size: 155
356279 TAAACACATT
* *
356289 AAGGTCAAATCTGCTATGTCTTCGATCTGCTCCCCTTCAAATACATAGATGCCAAATCATCTTGG
1 AAGGTCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCAAATACAGAGATGCCAAATCATCTTGG
* * * *
356354 ATCTGCTTCAATGAAGGTCCAATTTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATAC
66 ATCTGCTTCAATAAAGGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACAGAGATAC
356419 CAAATCATCTTGGATCTATTCAATG
131 CAAATCATCTTGGATCTATTCAATG
* * *
356444 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCAAATACAGAGATGCCAAATCATCTTGG
* ** *
356509 ATCTGCTTCAATAAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATG
66 ATCTGCTTCAATAAAGGTCCA-ATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACAGAGATA
356573 CCAAAT
130 CCAAAT
356579 ATGTTTCTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
154 2 0.02
155 119 0.98
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (155 bp):
AAGGTCAAATCTGCTATGTCTTCGATCTGCTCCCCGTCAAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATAAAGGTCCAATCTGCTATGTCTTCGATCTGCTCCCCGTCGAATACAGAGATAC
CAAATCATCTTGGATCTATTCAATG
Found at i:363326 original size:17 final size:18
Alignment explanation
Indices: 363304--363337 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
363294 GATATGATAC
*
363304 TAAAAT-TATTAAAAAAT
1 TAAAATATAATAAAAAAT
363321 TAAAATATAATAAAAAA
1 TAAAATATAATAAAAAA
363338 ATCAGGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATATAATAAAAAAT
Found at i:363636 original size:23 final size:22
Alignment explanation
Indices: 363593--363650 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
363583 AAAAGGTATC
* *
363593 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
363614 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
363637 TGCATATCATATCT
1 TACAAATCATATCT
363651 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:363653 original size:19 final size:18
Alignment explanation
Indices: 363629--363664 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
363619 AATCATATCT
363629 TCTAAGATTGCATATCATA
1 TCTAAGATTGCA-ATCATA
363648 TCTAAGATTGCAATCAT
1 TCTAAGATTGCAATCAT
363665 TGAAGATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
TCTAAGATTGCAATCATA
Found at i:363672 original size:16 final size:19
Alignment explanation
Indices: 363632--363672 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
363622 CATATCTTCT
*
363632 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
363651 AAGATTGCA-ATCAT-T-G
1 AAGATTGCATATCATATCG
363667 AAGATT
1 AAGATT
363673 ATATTTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.29
17 1 0.05
18 5 0.24
19 9 0.43
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:363787 original size:21 final size:20
Alignment explanation
Indices: 363750--363788 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
363740 TTGGACTTCG
**
363750 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
363770 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
363789 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:364272 original size:13 final size:13
Alignment explanation
Indices: 364250--364282 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
364240 AAGGGTTTGT
364250 TTAT-TAAACTAA
1 TTATCTAAACTAA
364262 TTATCTAAACTAA
1 TTATCTAAACTAA
*
364275 TTAACTAA
1 TTATCTAA
364283 TTTAACTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:365624 original size:11 final size:11
Alignment explanation
Indices: 365598--365638 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
365588 CTTTCCTTAT
*
365598 ATAATACATGAA
1 ATAATA-ATAAA
365610 ATAATAATAAA
1 ATAATAATAAA
365621 ATAATAATAAA
1 ATAATAATAAA
365632 AT-ATAAT
1 ATAATAAT
365639 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:369398 original size:13 final size:13
Alignment explanation
Indices: 369382--369406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369372 ATGTGATTTC
369382 GATATATGTGTGT
1 GATATATGTGTGT
369395 GATATATGTGTG
1 GATATATGTGTG
369407 CGAGTAAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (13 bp):
GATATATGTGTGT
Found at i:369685 original size:5 final size:5
Alignment explanation
Indices: 369675--369722 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
369665 ATAGAAGATA
369675 TTATT TTATT TTA-T TTAGTT TTA-- TTATT TTA-T TTATTT TTATT TTATT
1 TTATT TTATT TTATT TTA-TT TTATT TTATT TTATT TTA-TT TTATT TTATT
369723 AATTTAGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
3 3 0.08
4 8 0.22
5 18 0.49
6 8 0.22
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:369702 original size:23 final size:23
Alignment explanation
Indices: 369673--369728 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
369663 AAATAGAAGA
369673 TATTATTTTATTT-TATTTAGTTT
1 TATTATTTTATTTATATTTA-TTT
*
369696 TATTATTTTATTTATTTTTATTT
1 TATTATTTTATTTATATTTATTT
*
369719 TATTAATTTA
1 TATTATTTTA
369729 GGATTCGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTATTTTATTTATATTTATTT
Found at i:369703 original size:18 final size:18
Alignment explanation
Indices: 369680--369717 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
369670 AGATATTATT
369680 TTATTTTATTTAGTTTTA
1 TTATTTTATTTAGTTTTA
*
369698 TTATTTTATTTATTTTTA
1 TTATTTTATTTAGTTTTA
369716 TT
1 TT
369718 TTATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTATTTTATTTAGTTTTA
Found at i:371895 original size:26 final size:27
Alignment explanation
Indices: 371839--371895 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
371829 ACATATTATT
* * **
371839 TATTTTAAACTTTTACCGTATATTATT
1 TATTTCAAACTTTCACCGTATATTACC
*
371866 TATTTCAAACTTTCGCC-TATATTACC
1 TATTTCAAACTTTCACCGTATATTACC
371892 TATT
1 TATT
371896 CTAAAATTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.51
Consensus pattern (27 bp):
TATTTCAAACTTTCACCGTATATTACC
Found at i:375458 original size:45 final size:41
Alignment explanation
Indices: 375425--375524 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 41
375415 GATATATGTG
375425 GTTACGAGTAAGACCATGTCTGGGACATCGGCATCGTATTT
1 GTTACGAGTAAGACCATGTCTGGGACATCGGCATCGTATTT
* * * * *
375466 GTTTCGTGTAAGACCCTGTCTGGGATAGT-GGCATCGATATGT
1 GTTACGAGTAAGACCATGTCTGGGACA-TCGGCATCG-TATTT
375508 GATTAC-ATGTAAGACCA
1 G-TTACGA-GTAAGACCA
375525 CATCCGGAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 30 0.64
42 6 0.13
43 11 0.23
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (41 bp):
GTTACGAGTAAGACCATGTCTGGGACATCGGCATCGTATTT
Found at i:378958 original size:3 final size:3
Alignment explanation
Indices: 378945--378983 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
378935 TAAATAAATA
* *
378945 AAT AGAT AAT AAT AAT AAC AAT AAT AAC AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
378984 AGGCACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:380154 original size:13 final size:13
Alignment explanation
Indices: 380136--380173 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
380126 AATGTATTAC
380136 ACTATTTATTTTT
1 ACTATTTATTTTT
*
380149 ACTATTT-TTTCT
1 ACTATTTATTTTT
380161 ACTATTTATTTTT
1 ACTATTTATTTTT
380174 CGTGTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (13 bp):
ACTATTTATTTTT
Found at i:393370 original size:43 final size:43
Alignment explanation
Indices: 393309--393394 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
393299 ATGTTTGAAG
393309 TTAGATGAGATGGTGAATGCTCGCTATTACATTTTACATTGCA
1 TTAGATGAGATGGTGAATGCTCGCTATTACATTTTACATTGCA
393352 TTAGATGAGATGGTGAATGCTCGCTATTACATTTTACATTGCA
1 TTAGATGAGATGGTGAATGCTCGCTATTACATTTTACATTGCA
393395 GATTTGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (43 bp):
TTAGATGAGATGGTGAATGCTCGCTATTACATTTTACATTGCA
Found at i:398688 original size:5 final size:5
Alignment explanation
Indices: 398680--398709 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
398670 TGGAACACTC
398680 TATTT TATTT TATTT TATTT TATTT ATATT
1 TATTT TATTT TATTT TATTT TATTT -TATT
398710 AGGATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:399018 original size:12 final size:12
Alignment explanation
Indices: 399001--399025 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
398991 AAAATAGGGC
399001 TTTAGTGGCGTT
1 TTTAGTGGCGTT
399013 TTTAGTGGCGTT
1 TTTAGTGGCGTT
399025 T
1 T
399026 GAACAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TTTAGTGGCGTT
Found at i:399119 original size:41 final size:41
Alignment explanation
Indices: 399072--399150 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
399062 GTTTGCAATA
* *
399072 AAACGCCGCTAAAAACTGAGCAATAGCGGCGTTTTTGGTCC
1 AAACGCCGCTAAAAACTGAACAATAGCGGCGCTTTTGGTCC
399113 AAACGCCGCTAAAAACTGAACAATAGCGGCGCTTTTGG
1 AAACGCCGCTAAAAACTGAACAATAGCGGCGCTTTTGG
399151 AAAAACGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (41 bp):
AAACGCCGCTAAAAACTGAACAATAGCGGCGCTTTTGGTCC
Found at i:399181 original size:41 final size:41
Alignment explanation
Indices: 399136--399243 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
399126 AACTGAACAA
* *
399136 TAGCGGCGCTTTTGGAAAAACGCTGCTATAGGTCGAGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
* * *
399177 TAGCGGCGCTCTTGGAAAAATGCCGCTATAGATCGTGGTTT
1 TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
399218 TAGCGGCGCTTTTGGAAAAACGCCGC
1 TAGCGGCGCTTTTGGAAAAACGCCGC
399244 AAAAAAGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGAAAAACGCCGCTATAGATCGAGGTTT
Found at i:400168 original size:27 final size:26
Alignment explanation
Indices: 400130--400185 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
400120 TTGTAATATA
400130 TATATTTAGGGTTTAGGATATA-GGTT
1 TATATTTAGGGTTTA-GATATAGGGTT
* *
400156 TATAGTTTGGGGTTTAGATTTAGGGTT
1 TATA-TTTAGGGTTTAGATATAGGGTT
400183 TAT
1 TAT
400186 TGTTAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (26 bp):
TATATTTAGGGTTTAGATATAGGGTT
Found at i:400411 original size:17 final size:18
Alignment explanation
Indices: 400389--400422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
400379 TATTTGTTTT
400389 AATATA-TTAAAATTATC
1 AATATAGTTAAAATTATC
*
400406 AATATAGTTTAAATTAT
1 AATATAGTTAAAATTAT
400423 TTAAGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATAGTTAAAATTATC
Found at i:402152 original size:46 final size:46
Alignment explanation
Indices: 402085--402252 Score: 197
Period size: 46 Copynumber: 3.8 Consensus size: 46
402075 TGTAACCCGC
* *
402085 CCATAAGCGAACTCGGTCTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
402131 CCATAAGTGAACTCGGACTCAACTCAACGAGC-C-TA-GTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
402173 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
402216 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
402253 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
39 23 0.23
40 3 0.03
41 2 0.02
42 5 0.05
43 6 0.06
44 1 0.01
45 3 0.03
46 59 0.58
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:407764 original size:19 final size:19
Alignment explanation
Indices: 407742--407778 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
407732 TATAATATAG
407742 AAAATAAATATTATTTAAT
1 AAAATAAATATTATTTAAT
* *
407761 AAAATATATATTTTTTAA
1 AAAATAAATATTATTTAA
407779 AGGTTATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATAAATATTATTTAAT
Found at i:412419 original size:12 final size:13
Alignment explanation
Indices: 412393--412442 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
412383 AACATATTTA
412393 ATATAATGTTTTT
1 ATATAATGTTTTT
412406 ATATAATG-TTTT
1 ATATAATGTTTTT
412418 AT-T-AT-TTTTT
1 ATATAATGTTTTT
* *
412428 AAATAATTTTTTT
1 ATATAATGTTTTT
412441 AT
1 AT
412443 GTATTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 8 0.26
13 14 0.45
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATAATGTTTTT
Found at i:412433 original size:22 final size:20
Alignment explanation
Indices: 412401--412442 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
412391 TAATATAATG
*
412401 TTTTTATATAATGTTTTATTAT
1 TTTTTAAATAAT-TTTT-TTAT
412423 TTTTTAAATAATTTTTTTAT
1 TTTTTAAATAATTTTTTTAT
412443 GTATTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTAAATAATTTTTTTAT
Found at i:418913 original size:79 final size:79
Alignment explanation
Indices: 418789--418959 Score: 233
Period size: 79 Copynumber: 2.2 Consensus size: 79
418779 GGACTAAGAT
*
418789 CCGAAGGCATTTGTGCGAGATACATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGA-TACTA
1 CCGAAGGCATTTGTGCGAGATACAAATCCGGACTAAGATCCGAAGGCATTTGTGCGA-ATTACTA
*
418853 -ATTCCGGGCTAAG-C
65 TA-ACCGGGCTAAGTC
* **
418867 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAATTACT
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAATTACT
418931 ATAACCGGGCTAAGTC
64 ATAACCGGGCTAAGTC
418947 CCGAAGGCATTTG
1 CCGAAGGCATTTG
418960 AATGAGGAGC
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
78 24 0.29
79 44 0.53
80 15 0.18
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAATTACTAT
AACCGGGCTAAGTC
Found at i:418921 original size:40 final size:40
Alignment explanation
Indices: 418737--418959 Score: 253
Period size: 39 Copynumber: 5.7 Consensus size: 40
418727 TTGAATGATG
* * * *
418737 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
418776 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-ATA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
418815 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
418855 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
418894 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
418935 -CCGGGCTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
418960 AATGAGGAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 92 0.56
40 65 0.39
41 8 0.05
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:418981 original size:79 final size:79
Alignment explanation
Indices: 418828--418992 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
418818 GGACTAAGAT
* ** *
418828 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
418893 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
418907 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTAAGTCCCGAAGGCATTTGAATGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
418969 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
418986 CCGAAGG
1 CCGAAGG
418993 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 47 0.64
80 24 0.32
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:426634 original size:39 final size:39
Alignment explanation
Indices: 426590--426671 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
426580 AATTATGTTA
*
426590 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGACTTTAGCCCAGATACATTT
* * *
426629 CCAGCACGAAGCCTGCGGGTCTTTAGCCCAGATACCTTT
1 CCAGCACAAAGCCTGCGGGACTTTAGCCCAGATACATTT
426668 CCAG
1 CCAG
426672 TGTCTTGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (39 bp):
CCAGCACAAAGCCTGCGGGACTTTAGCCCAGATACATTT
Found at i:438866 original size:12 final size:12
Alignment explanation
Indices: 438849--438873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
438839 CCACACACGC
438849 CTGTGTGCTAGG
1 CTGTGTGCTAGG
438861 CTGTGTGCTAGG
1 CTGTGTGCTAGG
438873 C
1 C
438874 CGTGACAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (12 bp):
CTGTGTGCTAGG
Found at i:440718 original size:27 final size:26
Alignment explanation
Indices: 440674--441068 Score: 321
Period size: 27 Copynumber: 14.7 Consensus size: 26
440664 TTAGTTTACC
* * *
440674 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
*
440701 AAATTA-CTAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATA-CCCTGA-TTTGTA
440727 AAATTACCAAAATATCCCT-AGTTTGTA
1 AAATTACCAAAATA-CCCTGA-TTTGTA
* *
440754 AAATTACCAAAATACCCATGGTTTGTG
1 AAATTACCAAAATACCC-TGATTTGTA
*
440781 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATA-CCCTGATTTGTA
** *
440808 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
*
440835 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATA-CCCTGATTTGTA
* ** *
440862 AAGTTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
* **
440889 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCC-TGATTTGTA
440916 AAATTACCAAAATATCCCT-AGTTTGTA
1 AAATTACCAAAATA-CCCTGA-TTTGTA
440943 AAATTACCAAAATATCCCTGATTTGTA
1 AAATTACCAAAATA-CCCTGATTTGTA
* * * *
440970 AAATTATCGAAATACCCTTAGTTTGCA
1 AAATTACCAAAATACCCTGA-TTTGTA
*** *
440997 AAATTATTGAAATACTCTCGATTTGTA
1 AAATTACCAAAATACCCT-GATTTGTA
** * *
441024 AAATTACTGAAATACCGTCGACTTGTAA
1 AAATTACCAAAATACCCT-GATTTGT-A
*
441052 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
441069 CCGATTTACA
Statistics
Matches: 305, Mismatches: 47, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
25 1 0.00
26 32 0.10
27 245 0.80
28 27 0.09
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (26 bp):
AAATTACCAAAATACCCTGATTTGTA
Found at i:441121 original size:27 final size:27
Alignment explanation
Indices: 440870--441123 Score: 117
Period size: 27 Copynumber: 9.4 Consensus size: 27
440860 TGAAGTTACT
* ** *
440870 GAAATACCCTCGACTTGTAAAATTACC
1 GAAATACCCTCGATTTACAAAATTATC
* * * *
440897 AAAATACCCTTGGTTTACAAAATTACC
1 GAAATACCCTCGATTTACAAAATTATC
* * ** *
440924 AAAATATCCCTAG-TTTGTAAAATTACC
1 GAAATA-CCCTCGATTTACAAAATTATC
* **
440951 AAAATATCCCT-GATTTGTAAAATTATC
1 GAAATA-CCCTCGATTTACAAAATTATC
* * *
440978 GAAATACCCT-TAGTTTGCAAAATTATT
1 GAAATACCCTCGA-TTTACAAAATTATC
* **
441005 GAAATACTCTCGATTTGTAAAATTA-C
1 GAAATACCCTCGATTTACAAAATTATC
*
441031 TGAAATACCGTCGACTTGTA-AAAATTA-C
1 -GAAATACCCTCGA-TT-TACAAAATTATC
* * *
441059 CAAAGTACCCCCGATTTACAGAATTA-C
1 GAAA-TACCCTCGATTTACAAAATTATC
* ** *
441086 CATTTTACCCTCGATTTACAAAATTATT
1 GA-AATACCCTCGATTTACAAAATTATC
441114 GAAATACCCT
1 GAAATACCCT
441124 TGTAGGGTAG
Statistics
Matches: 183, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
26 8 0.04
27 150 0.82
28 24 0.13
29 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
GAAATACCCTCGATTTACAAAATTATC
Found at i:441137 original size:27 final size:27
Alignment explanation
Indices: 441107--441274 Score: 237
Period size: 27 Copynumber: 6.2 Consensus size: 27
441097 CGATTTACAA
*
441107 AATTATTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* * * *
441134 AATTACCGAAATACCCCTATTGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
441161 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* *
441188 AATTACTAAAATACCCTTGTAGGGAAG
1 AATTACTGAAATACCCTTGTAGGGTAG
*
441215 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAG
* * *
441242 AATTACCGAGATACCCTTGTAGGGTAA
1 AATTACTGAAATACCCTTGTAGGGTAG
441269 AATTAC
1 AATTAC
441275 CATTTTGCCC
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCCTTGTAGGGTAG
Found at i:441514 original size:25 final size:25
Alignment explanation
Indices: 441480--441574 Score: 172
Period size: 25 Copynumber: 3.8 Consensus size: 25
441470 AGGAAGTGTT
*
441480 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
441505 AAAAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
441530 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
441555 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
441575 ATTAAAAGAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:441587 original size:24 final size:25
Alignment explanation
Indices: 441480--441587 Score: 127
Period size: 25 Copynumber: 4.4 Consensus size: 25
441470 AGGAAGTGTT
*
441480 AAAAG-GGCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAGTTTATC
*
441504 GAAAAG-GGCTTTGCCCCAGTTTACC
1 -AAAAGAGGCTTTGCCCCAGTTTATC
441529 AAAA-AGGGCTTTGCCCCAGTTTATC
1 AAAAGA-GGCTTTGCCCCAGTTTATC
*
441554 AAAA-AGGGCTTTGCCCCAG-TTATT
1 AAAAGA-GGCTTTGCCCCAGTTTATC
441578 AAAAGAGGCT
1 AAAAGAGGCT
441588 AGGCCTCCAG
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
24 16 0.21
25 62 0.79
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGTTTATC
Found at i:441599 original size:50 final size:50
Alignment explanation
Indices: 441478--441587 Score: 154
Period size: 50 Copynumber: 2.2 Consensus size: 50
441468 GGAGGAAGTG
*
441478 TTAAAAG-GGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTA
1 TTAAAAGAGGCTTTGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTA
** *
441527 CCAAAA-AGGGCTTTGCCCCAGTTTATCAAAAAGGGCTTTGCCCCAG-TTA
1 TTAAAAGA-GGCTTTGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTA
441576 TTAAAAGAGGCT
1 TTAAAAGAGGCT
441588 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
49 15 0.29
50 37 0.71
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (50 bp):
TTAAAAGAGGCTTTGCCCCAGTTTACCAAAAAGGGCTTTGCCCCAGTTTA
Found at i:441830 original size:31 final size:30
Alignment explanation
Indices: 441795--441877 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
441785 CGTTTACAGT
*
441795 AAAGGCTTCGGCCCAGTGATATGATT-TATGA
1 AAAGGCTTCGGCCCAGT-ATATG-TTAAATGA
*
441826 AAAGGCTTCGGCACAGTA-ATAGTTAAATGA
1 AAAGGCTTCGGCCCAGTATAT-GTTAAATGA
*
441856 AAA-GCTTCGGCCTAGTATATGT
1 AAAGGCTTCGGCCCAGTATATGT
441878 CGAGACTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 18 0.40
30 11 0.24
31 16 0.36
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTATATGTTAAATGA
Found at i:442976 original size:104 final size:104
Alignment explanation
Indices: 442796--443005 Score: 393
Period size: 104 Copynumber: 2.0 Consensus size: 104
442786 AGAGTGCGCA
*
442796 GCGGTAGCGTAGTGGGGTAGATGTTACACGACTACCCTGTTAGTTAGAAATTTCGGGGACAAAAT
1 GCGGTAGCGTAGTGGGGTAGATGTTACACGACTACCCTGTTAGATAGAAATTTCGGGGACAAAAT
442861 TTCTTTAAGGGAGGTAGAGTTGTAACACCCTGAATTTGG
66 TTCTTTAAGGGAGGTAGAGTTGTAACACCCTGAATTTGG
* *
442900 GCGGTAGCGTAGTGGGGTAGATGTTACACGACTACCCTGTTAGATGGAAATTTCGGGGACGAAAT
1 GCGGTAGCGTAGTGGGGTAGATGTTACACGACTACCCTGTTAGATAGAAATTTCGGGGACAAAAT
442965 TTCTTTAAGGGAGGTAGAGTTGTAACACCCTGAATTTGG
66 TTCTTTAAGGGAGGTAGAGTTGTAACACCCTGAATTTGG
443004 GC
1 GC
443006 CTAAAAGTTT
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (104 bp):
GCGGTAGCGTAGTGGGGTAGATGTTACACGACTACCCTGTTAGATAGAAATTTCGGGGACAAAAT
TTCTTTAAGGGAGGTAGAGTTGTAACACCCTGAATTTGG
Found at i:443952 original size:27 final size:27
Alignment explanation
Indices: 443920--443982 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
443910 CTGGATTTAC
**
443920 AAAATTATTGAAATACCCCTGTAGGGT
1 AAAATTACCGAAATACCCCTGTAGGGT
* * * *
443947 AGAATTACCGAGATACCCTTGTGGGGT
1 AAAATTACCGAAATACCCCTGTAGGGT
443974 AAAATTACC
1 AAAATTACC
443983 ATTTTGCCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (27 bp):
AAAATTACCGAAATACCCCTGTAGGGT
Found at i:443992 original size:27 final size:28
Alignment explanation
Indices: 443962--444024 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 28
443952 TACCGAGATA
*
443962 CCCTTGTGGG-GTAAAATTACCATTTTG
1 CCCTTGTGGGTGTAAAATGACCATTTTG
* ***
443989 CCCTT-TGGGTGTTAAATGATTGTTTTG
1 CCCTTGTGGGTGTAAAATGACCATTTTG
444016 CCCTTGTGG
1 CCCTTGTGG
444025 CCAAGTGACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.14
27 22 0.76
28 3 0.10
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.41
Consensus pattern (28 bp):
CCCTTGTGGGTGTAAAATGACCATTTTG
Found at i:444221 original size:25 final size:25
Alignment explanation
Indices: 444187--444308 Score: 172
Period size: 25 Copynumber: 4.8 Consensus size: 25
444177 AGGAAGTGTT
*
444187 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
444212 AAAAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
* **
444237 AAAAGGGCTTTACCCCAGTTTACTG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* *
444262 AAAAGGGCTTTTTACCCCAGTTTATCA
1 AAAAGGGC--TTTGCCCCAGTTTACCA
444289 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
444309 ATTAAAAGAG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
25 65 0.75
27 22 0.25
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:444316 original size:50 final size:51
Alignment explanation
Indices: 444187--444308 Score: 192
Period size: 52 Copynumber: 2.4 Consensus size: 51
444177 AGGAAGTGTT
* *
444187 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGC-TTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACTGAAAAGGGCTTTTACCCCAGTTTACCA
* *
444237 AAAAGGGCTTTACCCCAGTTTACTGAAAAGGGCTTTTTACCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACTGAAAAGGGC-TTTTACCCCAGTTTACCA
444289 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
444309 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 31 0.48
52 34 0.52
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTTGCCCCAGTTTACTGAAAAGGGCTTTTACCCCAGTTTACCA
Found at i:444564 original size:31 final size:29
Alignment explanation
Indices: 444529--444611 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 29
444519 TGTTTACAGT
*
444529 AAAGGCTTCGGCCCAGTGATATGATT-TATGG
1 AAAGGCTTCGGCCCAGT-ATATG-TTAAAT-G
*
444560 AAAGGCTTCGGCCCAGTA-ACAGTTAAATG
1 AAAGGCTTCGGCCCAGTATA-TGTTAAATG
444589 AAAGGCTTCGGCCCAGTATATGT
1 AAAGGCTTCGGCCCAGTATATGT
444612 CGAGACTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 24 0.52
30 5 0.11
31 17 0.37
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (29 bp):
AAAGGCTTCGGCCCAGTATATGTTAAATG
Found at i:446493 original size:27 final size:27
Alignment explanation
Indices: 446462--446830 Score: 354
Period size: 27 Copynumber: 13.6 Consensus size: 27
446452 TTAGTTTACC
* *
446462 AAATTACTAAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
446489 AAATTACCAAAATACTCGT-GGTTTGTA
1 AAATTACCAAAATAC-CCTCGATTTGTA
*
446516 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* * *
446543 AAATTGCCAAAATACCC-CTAGTTTGTG
1 AAATTACCAAAATACCCTCGA-TTTGTA
446570 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
** *
446597 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
446624 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
446651 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **
446678 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
446705 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* * *
446732 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* **
446759 AAATTACTAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
** * * *
446786 AAATTACTGAAATACCTTAGACTTGTAA
1 AAATTACCAAAATACCCTCGATTTGT-A
*
446814 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
446831 CTGATTTACA
Statistics
Matches: 281, Mismatches: 50, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.01
27 259 0.92
28 20 0.07
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:446884 original size:27 final size:27
Alignment explanation
Indices: 446462--446873 Score: 273
Period size: 27 Copynumber: 15.2 Consensus size: 27
446452 TTAGTTTACC
* * *
446462 AAATTACTAAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
446489 AAATTACCAAAATACTCGT-GGTTTGTA
1 AAATTACCAAAATAC-CCTCGATTTATA
* *
446516 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * * *
446543 AAATTGCCAAAATACCC-CTAGTTTGTG
1 AAATTACCAAAATACCCTCGA-TTTATA
*
446570 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
** * *
446597 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
446624 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
446651 AAATTACTAAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
446678 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
446705 AAATTACCAAAATACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * * *
446732 AAATTATCGAAATACCCTCAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* ** *
446759 AAATTACTAAAATACCCTTAATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
** * *
446786 AAATTACTGAAATACCTTAGACTTGTA-A
1 AAATTACCAAAATACCCTCGA-TT-TATA
* *
446814 AAATTACCAAAGTACCC-CTGATTTACA
1 AAATTACCAAAATACCCTC-GATTTATA
* *** *
446841 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
446868 AAATTA
1 AAATTA
446874 TTGAAATACC
Statistics
Matches: 314, Mismatches: 56, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
26 4 0.01
27 284 0.90
28 25 0.08
29 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:446899 original size:27 final size:27
Alignment explanation
Indices: 446869--447037 Score: 203
Period size: 27 Copynumber: 6.3 Consensus size: 27
446859 CGATTTACAA
*
446869 AATTATTGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
*
446896 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
* * *
446923 AATTACTGAAATACCCTTGTAAGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
*
446950 AATTACTGAAATACCCTTATAGGGTAG
1 AATTACTGAAATACCCCTATAGGGTAG
* * *
446977 AATTACTAAAATACCCCTGTAGGGTAA
1 AATTACTGAAATACCCCTATAGGGTAG
* * * * * *
447004 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTATAGGGTAG
447031 AATTACT
1 AATTACT
447038 ATTTTGCCCT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 124 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (27 bp):
AATTACTGAAATACCCCTATAGGGTAG
Found at i:447047 original size:27 final size:27
Alignment explanation
Indices: 447017--447080 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
447007 TACCGAGATA
*
447017 CCCTTGTGGGGTAAAATTACTATTTTG
1 CCCTTGTGGGGTAAAATGACTATTTTG
* * * *
447044 CCCTTAG-GGTGTTAAATGATTGTTTTG
1 CCCTT-GTGGGGTAAAATGACTATTTTG
447071 CCCTTGTGGG
1 CCCTTGTGGG
447081 CAAGTGACAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 27 0.93
28 1 0.03
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (27 bp):
CCCTTGTGGGGTAAAATGACTATTTTG
Found at i:447049 original size:81 final size:81
Alignment explanation
Indices: 446867--447037 Score: 243
Period size: 81 Copynumber: 2.1 Consensus size: 81
446857 CTCGATTTAC
* * * * *
446867 AAAATTATTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACTGA
1 AAAATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAAAATTACCGA
446932 AATACCCTTGTAAGGT
66 AATACCCTTGTAAGGT
* * *
446948 AGAATTACTGAAATACCCTTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAAAATTACCGA
1 AAAATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAAAATTACCGA
* **
447013 GATACCCTTGTGGGGT
66 AATACCCTTGTAAGGT
447029 AAAATTACT
1 AAAATTACT
447038 ATTTTGCCCT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (81 bp):
AAAATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAAAATTACCGA
AATACCCTTGTAAGGT
Found at i:447276 original size:25 final size:25
Alignment explanation
Indices: 447242--447311 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
447232 AAGAAGTGCT
*
447242 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
447267 AAAAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
447292 AAAAGGGCTTTGCCTCAGTT
1 AAAAGGGCTTTGCCCCAGTT
447312 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:448212 original size:21 final size:19
Alignment explanation
Indices: 448187--448254 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
448177 GACTTTCAAT
448187 TCAAAGCTTCATAACTTATA
1 TCAAA-CTTCATAACTTATA
*
448207 TCCAAACTTCATAACTT-CA
1 T-CAAACTTCATAACTTATA
448226 T--AACTTCATAACTTATA
1 TCAAACTTCATAACTTATA
448243 TTCAAAGCTTCA
1 -TCAAA-CTTCA
448255 ATTTATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 13 0.32
17 1 0.03
18 1 0.03
19 2 0.05
20 14 0.35
21 9 0.22
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (19 bp):
TCAAACTTCATAACTTATA
Found at i:448224 original size:8 final size:8
Alignment explanation
Indices: 448211--448239 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
448201 CTTATATCCA
448211 AACTTCAT
1 AACTTCAT
448219 AACTTCAT
1 AACTTCAT
448227 AACTTCAT
1 AACTTCAT
448235 AACTT
1 AACTT
448240 ATATTCAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (8 bp):
AACTTCAT
Found at i:448489 original size:40 final size:40
Alignment explanation
Indices: 448387--448525 Score: 172
Period size: 40 Copynumber: 3.4 Consensus size: 40
448377 CGAATTCTCA
**
448387 CACACTAAGTGCCAATACATAGCCGAAGCTAT-TTTAATCTTG
1 CACACTAAGTGCC-ATACATAGCCGAAGCTATCTCGAATC--G
* * * *
448429 CATAGTAAGTGTCATACATAGCTGAAGCTATCTCGAATCG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
*
448469 CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATTG
1 CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
*
448509 CACACGAAGTGCCATAC
1 CACACTAAGTGCCATAC
448526 GTAATCGAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 52 0.62
41 17 0.20
42 15 0.18
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCCGAAGCTATCTCGAATCG
Found at i:474150 original size:86 final size:87
Alignment explanation
Indices: 474005--474182 Score: 331
Period size: 86 Copynumber: 2.1 Consensus size: 87
473995 TGCCGATTTT
*
474005 TTCAAAGCCAGGTCCTTCTATATTCTTTGTTTTTATTAAATCTGTGATTATCTTTTCTTAATCCT
1 TTCAAAGCCAGGTCCTTCTATATTCTTTGTTTTTATTAAATCTGCGATTATCTTTTCTTAATCCT
474070 AGATACCTGACGGCAATTCT-C
66 AGATACCTGACGGCAATTCTAC
*
474091 TTCAAAGCCAGGTCCTTCTATGTTCTTTGTTTTTATTAAATCTGCGATTATCTTTTCTTAATCCT
1 TTCAAAGCCAGGTCCTTCTATATTCTTTGTTTTTATTAAATCTGCGATTATCTTTTCTTAATCCT
474156 AGATACCTGACGGCAATTCTAC
66 AGATACCTGACGGCAATTCTAC
474178 TTCAA
1 TTCAA
474183 GGTCATAGTC
Statistics
Matches: 89, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 83 0.93
87 6 0.07
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (87 bp):
TTCAAAGCCAGGTCCTTCTATATTCTTTGTTTTTATTAAATCTGCGATTATCTTTTCTTAATCCT
AGATACCTGACGGCAATTCTAC
Found at i:478478 original size:26 final size:26
Alignment explanation
Indices: 478449--478501 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
478439 TCCAATTCAG
478449 GTACGTTTGAAATGTTTATCATGTTT
1 GTACGTTTGAAATGTTTATCATGTTT
478475 GTACGTTTGAAATGTTTATCATGTTT
1 GTACGTTTGAAATGTTTATCATGTTT
478501 G
1 G
478502 AGAATGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.21, T:0.49
Consensus pattern (26 bp):
GTACGTTTGAAATGTTTATCATGTTT
Found at i:497509 original size:40 final size:40
Alignment explanation
Indices: 497451--497573 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
497441 GGATTTAGAA
*
497451 GGATATAG-CAACTCGCACAAATGCCTTCGGGACTTAGCCC
1 GGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCC
* *
497491 GGATATAGTCACTAGCACAACTGCCTTCAGGACTTAGCCC
1 GGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
*
497531 GGATATAGTCACTAGCAC-CATGCCTTCGGGACTTAGCCC
1 GGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
497570 GGAT
1 GGAT
497574 GTTATCCGAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 22 0.29
40 53 0.70
41 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
GGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
Found at i:502209 original size:12 final size:12
Alignment explanation
Indices: 502192--502216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
502182 AAATTAAACT
502192 TATTTAATCAAA
1 TATTTAATCAAA
502204 TATTTAATCAAA
1 TATTTAATCAAA
502216 T
1 T
502217 TCATCCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTTAATCAAA
Found at i:506556 original size:53 final size:54
Alignment explanation
Indices: 506475--506682 Score: 177
Period size: 53 Copynumber: 3.9 Consensus size: 54
506465 TTTCCTTTTT
* * * * * *
506475 GAACTTACCATTGTCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* **
506528 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * ** * * * *
506582 GTAACTCATCAGTGTGATGTCTTGACATAGTCTTACATGATTTCCTTACCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * * * *
506637 TAACTTATCAATACCATGCATTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
506683 ATCTTACCAA
Statistics
Matches: 122, Mismatches: 29, Indels: 7
0.77 0.18 0.04
Matches are distributed among these distances:
52 2 0.02
53 43 0.35
54 36 0.30
55 39 0.32
56 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:506713 original size:47 final size:47
Alignment explanation
Indices: 506661--506829 Score: 284
Period size: 47 Copynumber: 3.6 Consensus size: 47
506651 CATGCATTGG
* *
506661 CATGGTCTTACATGATATCCTTATCTTACCAAATTCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
* *
506708 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCGTGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
* *
506755 CATGGTTTTACATGGTATCCTTGTTTTACCAAATTCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
506802 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
506830 GTGCCAATGC
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 112 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.38
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATTCCATGTTCCAAA
Found at i:508765 original size:31 final size:31
Alignment explanation
Indices: 508730--508793 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
508720 CCTTTTCATA
*
508730 TTTCATATTTCATAACACTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
***
508761 TTTCATATTTCATGTTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
508792 TT
1 TT
508794 ACTATAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:509035 original size:25 final size:25
Alignment explanation
Indices: 509007--509098 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
508997 GCCTAGCCTC
*
509007 TTTTAATAACTGGGGCAAAAGCCCT
1 TTTTGATAACTGGGGCAAAAGCCCT
**
509032 TTTTGATAAAC-ACGGCAAAAGCCCT
1 TTTTGAT-AACTGGGGCAAAAGCCCT
*
509057 TTTCGGGA-AACTGGGGC-AAAGCCCT
1 TTT--TGATAACTGGGGCAAAAGCCCT
*
509082 TTTCTG-TAACTGAGGCA
1 TTT-TGATAACTGGGGCA
509099 TAGCCCATTT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
24 9 0.17
25 35 0.67
26 6 0.12
27 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (25 bp):
TTTTGATAACTGGGGCAAAAGCCCT
Found at i:509098 original size:24 final size:25
Alignment explanation
Indices: 509049--509104 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
509039 AAACACGGCA
*
509049 AAAGCCCTTTTCGGGAAACTGGGGC
1 AAAGCCCTTTTCGGGAAACTGAGGC
* *
509074 AAAGCCCTTTTC-TGTAACTGAGGC
1 AAAGCCCTTTTCGGGAAACTGAGGC
*
509098 ATAGCCC
1 AAAGCCC
509105 ATTTGCACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (25 bp):
AAAGCCCTTTTCGGGAAACTGAGGC
Found at i:509280 original size:24 final size:24
Alignment explanation
Indices: 509239--509284 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
509229 ATAATTAAAC
* * *
509239 CCTAGGGGTATAATAGTCATTTTA
1 CCTAGGGGCAAAACAGTCATTTTA
509263 CCTAGGGGCAAAACAGTCATTT
1 CCTAGGGGCAAAACAGTCATTT
509285 CCATATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (24 bp):
CCTAGGGGCAAAACAGTCATTTTA
Found at i:519760 original size:25 final size:26
Alignment explanation
Indices: 519745--519840 Score: 119
Period size: 26 Copynumber: 3.8 Consensus size: 26
519735 CTCTTTTAAT
*
519745 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
519771 AACTGGGGGAAAAGCCCTTTTCGATA
1 AACTGGGGCAAAAGCCCTTTTCGATA
*
519797 AACTAGGGC-AAAGCCCTTTTCTG-T-
1 AACTGGGGCAAAAGCCCTTTTC-GATA
*
519821 AACTGGGGC-ATAGCCCTTTT
1 AACTGGGGCAAAAGCCCTTTT
519841 GCACTTCCTC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
24 18 0.29
25 13 0.21
26 32 0.51
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (26 bp):
AACTGGGGCAAAAGCCCTTTTCGATA
Found at i:525450 original size:43 final size:41
Alignment explanation
Indices: 525356--525476 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 41
525346 GATTTGAGAT
* *
525356 TTACATGTAAGAACTGTCTGGGAC-ATCGGTATTGTATATGA
1 TTACATGTAAGACCTGTCTGGGACAAT-GGCATTGTATATGA
* * *
525397 TTTCGTGTAAGACCTTGTCTGGGACAATGGCATTGATATTTGA
1 TTACATGTAAGACC-TGTCTGGGACAATGGCATTG-TATATGA
* * *
525440 TTACATGTAAGACCACGTCTGAGACATTGGCATTGTA
1 TTACATGTAAGACC-TGTCTGGGACAATGGCATTGTA
525477 CGAGTTTTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
41 11 0.17
42 18 0.27
43 37 0.56
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (41 bp):
TTACATGTAAGACCTGTCTGGGACAATGGCATTGTATATGA
Found at i:528955 original size:81 final size:82
Alignment explanation
Indices: 528810--529165 Score: 436
Period size: 81 Copynumber: 4.4 Consensus size: 82
528800 TGGGCCATGT
* * * *
528810 ATGACTGAAATAACCCCATAGGGTAAAATGACCGAAATACCCC-TATAGGGTGAAATGACTGAAA
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTTATAGGGTAAAATGACCGAAA
* *
528874 TACCCCCATAAGGTGAA
66 TACCCCCGTAAGGTAAA
* * *
528891 ATGACCGAAATACCCCCATAGGGTAAAATGACCAAAATA-CCCTTATAGGATAAAATAACCGAAA
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTTATAGGGTAAAATGACCGAAA
528955 TACCCCCGTAAGGTAAA
66 TACCCCCGTAAGGTAAA
* *
528972 ATGACCGAAATACCCCCATAGAGTAAAATGACCGAAATACCCCTGTA-A-GGTAAAATGACCAAA
1 ATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCT-TATAGGGTAAAATGACCGAA
* *
529035 ATACCCTCGTAGGGTAAA
65 ATACCCCCGTAAGGTAAA
* **
529053 ATGACCGAAATACCCTCAT-GAGGTAAAATGACCGAAATACCCCTT-TAGGGTAAAATGATTGAA
1 ATGACCGAAATACCCCCATAG-GGTAAAATGACCGAAATACCCCTTATAGGGTAAAATGACCGAA
* *
529116 ATACCCCTGTAAGATAAA
65 ATACCCCCGTAAGGTAAA
* * * ** *
529134 ATAACTGTAATACCCCTGTAAGGTAAAATGAC
1 ATGACCGAAATACCCCCATAGGGTAAAATGAC
529166 TGATTTGCCC
Statistics
Matches: 236, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
80 6 0.03
81 223 0.94
82 5 0.02
83 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (82 bp):
ATGACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCTTATAGGGTAAAATGACCGAAA
TACCCCCGTAAGGTAAA
Found at i:529123 original size:27 final size:27
Alignment explanation
Indices: 528810--529165 Score: 369
Period size: 27 Copynumber: 13.2 Consensus size: 27
528800 TGGGCCATGT
*
528810 ATGACTGAAATAACCCC-ATAGGGTAAA
1 ATGACCGAAAT-ACCCCTATAGGGTAAA
*
528837 ATGACCGAAATACCCCTATAGGGTGAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * *
528864 ATGACTGAAATACCCCCATAAGGTGAA
1 ATGACCGAAATACCCCTATAGGGTAAA
*
528891 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * *
528918 ATGACCAAAATACCCTTATAGGATAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* ** *
528945 ATAACCGAAATACCCCCGTAAGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
528972 ATGACCGAAATACCCCCATAGAGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
528999 ATGACCGAAATACCCCTGTAAGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* *
529026 ATGACCAAAATA-CCCTCGTAGGGTAAA
1 ATGACCGAAATACCCCT-ATAGGGTAAA
529053 ATGACCGAAATA-CCCTCAT-GAGGTAAA
1 ATGACCGAAATACCCCT-ATAG-GGTAAA
*
529080 ATGACCGAAATACCCCTTTAGGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
** * * *
529107 ATGATTGAAATACCCCTGTAAGATAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
* * * * *
529134 ATAACTGTAATACCCCTGTAAGGTAAA
1 ATGACCGAAATACCCCTATAGGGTAAA
529161 ATGAC
1 ATGAC
529166 TGATTTGCCC
Statistics
Matches: 282, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.04
27 267 0.95
28 5 0.02
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
ATGACCGAAATACCCCTATAGGGTAAA
Found at i:529356 original size:36 final size:36
Alignment explanation
Indices: 529311--529381 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
529301 GTACTGATAT
* * *
529311 GGTTACACGGGTCGCCCAAGACGACTGTGGACCTAA
1 GGTTACACGGGTCACCCAAGACAACTATGGACCTAA
* *
529347 GGTTGCACGGGTCACCCAAGGCAACTATGGACCTA
1 GGTTACACGGGTCACCCAAGACAACTATGGACCTA
529382 CTGATGACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (36 bp):
GGTTACACGGGTCACCCAAGACAACTATGGACCTAA
Found at i:535204 original size:68 final size:69
Alignment explanation
Indices: 535071--535205 Score: 227
Period size: 68 Copynumber: 2.0 Consensus size: 69
535061 ATTAGTGCAT
* * *
535071 GTAATCAAAGGGGTGGACTTGCATGTCAATTTCCCCCATTTAATTAGTAGTGGCCGGCCATGACA
1 GTAATAAAAAGGGTGGACTTGCATGTCAATTTCCCCCACTTAATTAGTAGTGGCCGGCCATGACA
535136 ATAA
66 ATAA
*
535140 GTAATAAAAAGGGTGGACTTGCATGTCAATTT-CCCCACTTAATTGGTAGTGGCCGGCCATGACA
1 GTAATAAAAAGGGTGGACTTGCATGTCAATTTCCCCCACTTAATTAGTAGTGGCCGGCCATGACA
535204 AT
66 AT
535206 GAGGGTGGAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 32 0.52
69 30 0.48
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (69 bp):
GTAATAAAAAGGGTGGACTTGCATGTCAATTTCCCCCACTTAATTAGTAGTGGCCGGCCATGACA
ATAA
Found at i:536768 original size:242 final size:241
Alignment explanation
Indices: 536343--536820 Score: 857
Period size: 242 Copynumber: 2.0 Consensus size: 241
536333 AAGTAGAAGA
* *
536343 GAAATATGGTTGTTGTTCATGTTATTTGGATGAAAAATGGTAGTAAGGTGAAGTGCAAATGTTAG
1 GAAATATGGTTGTTGTTCATGTTATTTGCATGAAAAATGGTAGTAAGGTGAAGTGCAAATATTAG
* * *
536408 TATTTGATTACTAGTGTATATATGTGTATTAGCCGAGTTTTGAACTTGAGACAAAATGGTATGTA
66 TATTTGATTACTAGTGTACATATGTGTATTAGCCGAGTTTTGAACTTGAAACAAAATGGCATGTA
* *
536473 GTCAATACAAGTAACCATATTTGTAGGAAGTATTAAGCATATAATTGGCCTCAACATAGACATGC
131 ATCAATACAAGTAACCATATTTGTAGGAAGTATTAAGCATATAATCGGCCTCAACATAGACATGC
536538 ATATTCGGCCACATGAGATAGATTGGTGTAGCATGTATTCGGAGTAG
196 AT-TTCGGCCACATGAGATAGATTGGTGTAGCATGTATTCGGAGTAG
*
536585 GAAATATGGTTGTTGTTCATGTTATTTGCATGAGAAATGGTAGTAAGGTGAAGTGCAAATATTAG
1 GAAATATGGTTGTTGTTCATGTTATTTGCATGAAAAATGGTAGTAAGGTGAAGTGCAAATATTAG
536650 TATTTGATTACTAGTGTACATATGTGTATTAGCCGAGTTTTGAACTTGAAACAAAATGGCATGTA
66 TATTTGATTACTAGTGTACATATGTGTATTAGCCGAGTTTTGAACTTGAAACAAAATGGCATGTA
*
536715 ATTAATACAAGTAACCATATTTGTAGGAAGTATTAAGCATATAATCGGCCTCAACATAGACATGC
131 ATCAATACAAGTAACCATATTTGTAGGAAGTATTAAGCATATAATCGGCCTCAACATAGACATGC
*
536780 ATTTCGGCCACATGAGATAGATTGGTGTTGCATGTATTCGG
196 ATTTCGGCCACATGAGATAGATTGGTGTAGCATGTATTCGG
536821 TTAGGGGCAA
Statistics
Matches: 226, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
241 38 0.17
242 188 0.83
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.33
Consensus pattern (241 bp):
GAAATATGGTTGTTGTTCATGTTATTTGCATGAAAAATGGTAGTAAGGTGAAGTGCAAATATTAG
TATTTGATTACTAGTGTACATATGTGTATTAGCCGAGTTTTGAACTTGAAACAAAATGGCATGTA
ATCAATACAAGTAACCATATTTGTAGGAAGTATTAAGCATATAATCGGCCTCAACATAGACATGC
ATTTCGGCCACATGAGATAGATTGGTGTAGCATGTATTCGGAGTAG
Found at i:537397 original size:242 final size:242
Alignment explanation
Indices: 536972--537457 Score: 972
Period size: 242 Copynumber: 2.0 Consensus size: 242
536962 AATTGTATTA
536972 AATTGCTCAATGTGATTAAAAATGCGTATGACCACTTTGTATTTGAGCTAAAGGTGGCCATATGA
1 AATTGCTCAATGTGATTAAAAATGCGTATGACCACTTTGTATTTGAGCTAAAGGTGGCCATATGA
537037 CCTATCAACTCCTTGTCATATTCGGCCATAAGCTAGCATAATGAGACTTTAATAAGTTAAATTTG
66 CCTATCAACTCCTTGTCATATTCGGCCATAAGCTAGCATAATGAGACTTTAATAAGTTAAATTTG
537102 CTTGAATTAGCTCAAGAGCTTAGAGGACCAAAGTTGGACAAGGGAAAGGAAAAAGTGATCGAATA
131 CTTGAATTAGCTCAAGAGCTTAGAGGACCAAAGTTGGACAAGGGAAAGGAAAAAGTGATCGAATA
537167 GCCGCCGAAATCGTTCGACAACATCCGAAGTAAGTTTTCGAGTAATG
196 GCCGCCGAAATCGTTCGACAACATCCGAAGTAAGTTTTCGAGTAATG
537214 AATTGCTCAATGTGATTAAAAATGCGTATGACCACTTTGTATTTGAGCTAAAGGTGGCCATATGA
1 AATTGCTCAATGTGATTAAAAATGCGTATGACCACTTTGTATTTGAGCTAAAGGTGGCCATATGA
537279 CCTATCAACTCCTTGTCATATTCGGCCATAAGCTAGCATAATGAGACTTTAATAAGTTAAATTTG
66 CCTATCAACTCCTTGTCATATTCGGCCATAAGCTAGCATAATGAGACTTTAATAAGTTAAATTTG
537344 CTTGAATTAGCTCAAGAGCTTAGAGGACCAAAGTTGGACAAGGGAAAGGAAAAAGTGATCGAATA
131 CTTGAATTAGCTCAAGAGCTTAGAGGACCAAAGTTGGACAAGGGAAAGGAAAAAGTGATCGAATA
537409 GCCGCCGAAATCGTTCGACAACATCCGAAGTAAGTTTTCGAGTAATG
196 GCCGCCGAAATCGTTCGACAACATCCGAAGTAAGTTTTCGAGTAATG
537456 AA
1 AA
537458 ACTTAGTTTA
Statistics
Matches: 244, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 244 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (242 bp):
AATTGCTCAATGTGATTAAAAATGCGTATGACCACTTTGTATTTGAGCTAAAGGTGGCCATATGA
CCTATCAACTCCTTGTCATATTCGGCCATAAGCTAGCATAATGAGACTTTAATAAGTTAAATTTG
CTTGAATTAGCTCAAGAGCTTAGAGGACCAAAGTTGGACAAGGGAAAGGAAAAAGTGATCGAATA
GCCGCCGAAATCGTTCGACAACATCCGAAGTAAGTTTTCGAGTAATG
Found at i:537811 original size:40 final size:40
Alignment explanation
Indices: 537754--537877 Score: 178
Period size: 40 Copynumber: 3.1 Consensus size: 40
537744 CTAATGGGGT
* *
537754 TAAGTCCCGAAGACATTTGTGCTAGTGATTA-ATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTATA-TCCGGGC
* *
537794 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGC
* *
537834 TAAGTCCCGAAGGCATTTGTGGTAGTGACCATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGC
537874 TAAG
1 TAAG
537878 ACCCAACGGC
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
40 74 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGC
Found at i:544141 original size:42 final size:43
Alignment explanation
Indices: 544080--544177 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 43
544070 GATTTGAGAT
*
544080 TTACATGTAAGACCATGTCTAGGACATCGGTATCG-TATTTGA
1 TTACATGTAAGACCATGTCTAGGACATCGGCATCGATATTTGA
* * * *
544122 TTTCGTGTAAGACCCTGTCTAGGACATTGGCATCGATATTTGA
1 TTACATGTAAGACCATGTCTAGGACATCGGCATCGATATTTGA
544165 TTACATGTAAGAC
1 TTACATGTAAGAC
544178 AACGTCTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (43 bp):
TTACATGTAAGACCATGTCTAGGACATCGGCATCGATATTTGA
Found at i:544195 original size:43 final size:43
Alignment explanation
Indices: 544027--544197 Score: 143
Period size: 43 Copynumber: 4.0 Consensus size: 43
544017 ATATGATTCT
* * * ** *
544027 GATATGTGATTTCGTGTAAGACCACGTCT-GAGATGTTGGCGTC
1 GATATTTGATTACATGTAAGACCACGTCTAG-GACATTGGCATC
* * * *
544070 GAT-TTGAGATTTACATGTAAGACCATGTCTAGGACATCGGTATC
1 GATATT-TGA-TTACATGTAAGACCACGTCTAGGACATTGGCATC
* *
544114 G-TATTTGATTTCGTGTAAGACC-CTGTCTAGGACATTGGCATC
1 GATATTTGATTACATGTAAGACCAC-GTCTAGGACATTGGCATC
* * *
544156 GATATTTGATTACATGTAAGACAACGTCTGGGACGTTGGCAT
1 GATATTTGATTACATGTAAGACCACGTCTAGGACATTGGCAT
544198 TGTACGAGTT
Statistics
Matches: 100, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
42 30 0.30
43 41 0.41
44 28 0.28
45 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCACGTCTAGGACATTGGCATC
Found at i:549430 original size:28 final size:27
Alignment explanation
Indices: 549366--549520 Score: 229
Period size: 27 Copynumber: 5.7 Consensus size: 27
549356 TTATTAAGTC
* *
549366 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
549393 CGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCA-ACT
* *
549421 CGCACACTTAGAGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
549448 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
549476 CGCACACTTAGTGCTACATATTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
549503 CGCACACTTAGTGCTACA
1 CGCACACTTAGTGCTACA
549521 CAATTTAAAC
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 68 0.57
28 51 0.43
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:549450 original size:55 final size:55
Alignment explanation
Indices: 549366--549542 Score: 246
Period size: 55 Copynumber: 3.2 Consensus size: 55
549356 TTATTAAGTC
* * *
549366 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * *
549421 CGCACACTTAGAGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * *
549476 CGCACACTTAGTGCTACATATTCAATTCGCACACTTAGTGCTACACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAA-TCAAACT
549532 CGCACACTTAG
1 CGCACACTTAG
549543 CGCCAATCTC
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
55 92 0.85
56 16 0.15
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:552863 original size:43 final size:43
Alignment explanation
Indices: 552815--552972 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
552805 GTTACCTAGA
*
552815 TGTGATTACATGTAAGATCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
*
552858 TGTGATTACATGTAAGACCATGTCTGAGACATTGGCATCAT-TAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAT
* * * * *
552902 T-CGATTTCATGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
** *
552943 ATGTGACGACATGTAAGACCATATCTGGGA
1 -TGTGATTACATGTAAGACCATGTCTGGGA
552973 TATGGCTTTG
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 88 0.92
44 4 0.04
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:555399 original size:40 final size:40
Alignment explanation
Indices: 555350--555452 Score: 170
Period size: 40 Copynumber: 2.6 Consensus size: 40
555340 TGTTTTAATT
*
555350 TCGCACACTAAGTGTCATACATAGCCGAAGCTATCTCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
*
555390 TCGCACACTAAGTGCCATACATAGTCGAAGCTATCTCGAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
**
555430 TTACACACTAAGTGCCATACATA
1 TCGCACACTAAGTGCCATACATA
555453 ACTGAATTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCGAA
Found at i:564997 original size:21 final size:22
Alignment explanation
Indices: 564960--565006 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
564950 ATAATTTTCA
* *
564960 TTTT-TTTCATGTTCAAGTTTT
1 TTTTATTTCATGTACAAGATTT
564981 TTTTATTTCAT-TACAAGATTT
1 TTTTATTTCATGTACAAGATTT
*
565002 CTTTA
1 TTTTA
565007 CTCCATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTATTTCATGTACAAGATTT
Found at i:566306 original size:17 final size:17
Alignment explanation
Indices: 566284--566317 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
566274 GATGAGGAGG
*
566284 CCTACGAGGGCATTCCT
1 CCTACGAGGCCATTCCT
566301 CCTACGAGGCCATTCCT
1 CCTACGAGGCCATTCCT
566318 GATGATGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.38, G:0.21, T:0.24
Consensus pattern (17 bp):
CCTACGAGGCCATTCCT
Found at i:570652 original size:14 final size:15
Alignment explanation
Indices: 570633--570662 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
570623 TTTAAATTGA
570633 TTGAAATT-TATGAT
1 TTGAAATTGTATGAT
570647 TTGAAATTGTATGAT
1 TTGAAATTGTATGAT
570662 T
1 T
570663 GTTTGTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TTGAAATTGTATGAT
Found at i:574085 original size:65 final size:65
Alignment explanation
Indices: 573951--574072 Score: 190
Period size: 65 Copynumber: 1.9 Consensus size: 65
573941 ACCGCGGCTT
*
573951 TTTGTGAGCATCCTGTTATATGATCGGTTGTGATCCTACATATATTGCGGACACAAACACAGCTC
1 TTTGTGAGCATCCTGTTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAACACAGCTC
* * ** *
574016 TTTGTGAGCGTCCTGTTCTATGATCGGTTGTGATTTTGCATATATTGCAGACACAAA
1 TTTGTGAGCATCCTGTTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAA
574073 TGTAGTTCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 51 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (65 bp):
TTTGTGAGCATCCTGTTATATGATCGGTTGTGATCCTACATATATTGCAGACACAAACACAGCTC
Found at i:574172 original size:26 final size:25
Alignment explanation
Indices: 574134--574198 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
574124 TGGCTATCCG
574134 GAGCTT-CTGATTAAAGTCTCTTTGT
1 GAGCTTCCTGATTAAAGT-TCTTTGT
574159 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATT-AAAGTTCTTTGT
*
574185 GAACTTCCTGATTA
1 GAGCTTCCTGATTA
574199 TGGCTTGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
25 7 0.19
26 25 0.68
27 5 0.14
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (25 bp):
GAGCTTCCTGATTAAAGTTCTTTGT
Found at i:593963 original size:26 final size:27
Alignment explanation
Indices: 593898--593988 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
593888 ACTGATTTCA
* * *
593898 CACACTTAGTGCTCAGAAATTAATTCACG
1 CACACTTAGTGCTCAG-AATCAA-ACTCG
* *
593927 CACA--TAGTGCTTA-AATCCAACTCG
1 CACACTTAGTGCTCAGAATCAAACTCG
* *
593951 CACACTTAGTGCTCAGTATCAAATTCG
1 CACACTTAGTGCTCAGAATCAAACTCG
593978 CACACTTAGTG
1 CACACTTAGTG
593989 TATCCCTCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 7 0.14
25 4 0.08
26 8 0.16
27 27 0.54
29 4 0.08
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (27 bp):
CACACTTAGTGCTCAGAATCAAACTCG
Found at i:595308 original size:39 final size:40
Alignment explanation
Indices: 595210--595430 Score: 238
Period size: 39 Copynumber: 5.6 Consensus size: 40
595200 AATGATCTCT
* * *
595210 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC
*
595250 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC
*
595290 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* * * *
595329 GGGCTAAG-CCTGAAGGCATTGGTACGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
* *
595368 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC
* * *
595408 GAGCTATGTCCCAAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
595431 AACGAGTAGC
Statistics
Matches: 156, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 73 0.47
40 73 0.47
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC
Found at i:595452 original size:79 final size:79
Alignment explanation
Indices: 595275--595463 Score: 206
Period size: 79 Copynumber: 2.4 Consensus size: 79
595265 GGCATTTGTG
* * * *
595275 CGAGTTACTAATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAATTCCGGGCTAAGCC
1 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAATACCGAGCTAAGCC
** *
595339 TGAAGGCATTGGTA
66 CAAAGGCATTGGAA
* *
595353 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGAGCTATGT
1 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAAT-ACCGAGCTAAG-
*
595417 CCCAAAGGCATTTGAA
64 CCCAAAGGCATTGGAA
* * *
595433 CGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
595464 TACGTGATTC
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
78 23 0.24
79 48 0.51
80 23 0.24
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25
Consensus pattern (79 bp):
CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTGGTGCGAGTTACTAATACCGAGCTAAGCC
CAAAGGCATTGGAA
Found at i:595651 original size:30 final size:30
Alignment explanation
Indices: 595615--595701 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 30
595605 TACCGGCCTT
595615 TGGCTAAGTTGATCTTTGTGTATGAATATA
1 TGGCTAAGTTGATCTTTGTGTATGAATATA
**** **
595645 TGGCTAAGTTGATCTTT-TACCGGCCT-T-
1 TGGCTAAGTTGATCTTTGTGTATGAATATA
595672 TGGCTAAGTTGATCTTTGTGTATGAATATA
1 TGGCTAAGTTGATCTTTGTGTATGAATATA
595702 AGGGTTGGTA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
27 17 0.40
28 4 0.10
29 4 0.10
30 17 0.40
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (30 bp):
TGGCTAAGTTGATCTTTGTGTATGAATATA
Found at i:600032 original size:24 final size:24
Alignment explanation
Indices: 600005--600089 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 24
599995 TTGGAGGCCT
600005 AGCCTCTTTTAAT-AACTGGGGAAA
1 AGCC-CTTTTAATAAACTGGGGAAA
* *
600029 AGCCCTTTCTGATAAACTGGGGCAA
1 AGCCCTTT-TAATAAACTGGGGAAA
** * *
600054 AGCCCCTTTTCGGTAAACTGGGGCAG
1 AG-CCCTTTT-AATAAACTGGGGAAA
600080 AGCCCTTTTA
1 AGCCCTTTTA
600090 GCACTTCCTC
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.08
24 7 0.13
25 20 0.38
26 21 0.40
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (24 bp):
AGCCCTTTTAATAAACTGGGGAAA
Found at i:600070 original size:26 final size:26
Alignment explanation
Indices: 600018--600088 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
600008 CTCTTTTAAT
*
600018 AACTGGGGAAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCTGATA
*
600043 AACTGGGGCAAAGCCCCTTTTC-GGTA
1 AACTGGGGCAAAG-CCCTTTTCTGATA
*
600069 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
600089 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 19 0.46
26 18 0.44
27 4 0.10
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTCTGATA
Found at i:600919 original size:27 final size:27
Alignment explanation
Indices: 600889--600953 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
600879 GGGCATATTC
600889 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
600916 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
600943 GTCTTTTTACC
1 GTCATTTTACC
600954 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:601109 original size:27 final size:27
Alignment explanation
Indices: 600985--601220 Score: 186
Period size: 27 Copynumber: 8.7 Consensus size: 27
600975 TGCATCCTAC
* * * * *
600985 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTCGGTAATTTTACAAACT
** * ** *
601012 AAGGGTATTTCAATAGTTTTGTAAACC
1 AAGGGTATTTCGGTAATTTTACAAACT
* ** * *
601039 AATGGTATTTCTATAATTTTTAAAAAGT
1 AAGGGTATTTCGGTAA-TTTTACAAACT
* * * *
601067 CAATGGTATTTCTGTAATTTTATAAATT
1 -AAGGGTATTTCGGTAATTTTACAAACT
** *
601095 AAGGGTATTTTTGTAATTTTACAAATT
1 AAGGGTATTTCGGTAATTTTACAAACT
* *
601122 GAGGGTATTTCGGTAATTTCACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACT
601149 -AGTGGTATTTCGGTAATTTTACAAACT
1 AAG-GGTATTTCGGTAATTTTACAAACT
*
601176 AAGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACT
* *
601203 AGGGGTATTTTGGTAATT
1 AAGGGTATTTCGGTAATT
601221 CTATCCTACA
Statistics
Matches: 175, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 140 0.80
28 18 0.10
29 15 0.09
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTCGGTAATTTTACAAACT
Found at i:601180 original size:81 final size:81
Alignment explanation
Indices: 601070--601220 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
601060 AAAAAGTCAA
* * * * *
601070 TGGTATTTCTGTAATTTTATAAATTAAGGGTATTTTTGTAATTTTACAAA-TTGAGGGTATTTCG
1 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCG
601134 GTAATTTCACAAACTAG
65 GTAATTTCACAAACTAG
*
601151 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGG
601216 TAATT
66 TAATT
601221 CTATCCTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 61 0.97
82 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (81 bp):
TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGG
TAATTTCACAAACTAG
Found at i:601961 original size:27 final size:27
Alignment explanation
Indices: 601837--602072 Score: 186
Period size: 27 Copynumber: 8.7 Consensus size: 27
601827 TGCATCCTAC
* * * * *
601837 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTCGGTAATTTTACAAACT
** * ** *
601864 AAGGGTATTTCAATAGTTTTGTAAACC
1 AAGGGTATTTCGGTAATTTTACAAACT
* ** * *
601891 AATGGTATTTCTATAATTTTTAAAAAGT
1 AAGGGTATTTCGGTAA-TTTTACAAACT
* * * *
601919 CAATGGTATTTCTGTAATTTTATAAATT
1 -AAGGGTATTTCGGTAATTTTACAAACT
** *
601947 AAGGGTATTTTTGTAATTTTACAAATT
1 AAGGGTATTTCGGTAATTTTACAAACT
* *
601974 GAGGGTATTTCGGTAATTTCACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACT
602001 -AGTGGTATTTCGGTAATTTTACAAACT
1 AAG-GGTATTTCGGTAATTTTACAAACT
*
602028 AAGGGTATTTTGGTAATTTTACAAACT
1 AAGGGTATTTCGGTAATTTTACAAACT
* *
602055 AGGGGTATTTTGGTAATT
1 AAGGGTATTTCGGTAATT
602073 CTATCCTACA
Statistics
Matches: 175, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
26 2 0.01
27 140 0.80
28 18 0.10
29 15 0.09
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTCGGTAATTTTACAAACT
Found at i:602027 original size:852 final size:848
Alignment explanation
Indices: 600383--602083 Score: 3305
Period size: 852 Copynumber: 2.0 Consensus size: 848
600373 TCAAATTCGG
600383 GCTTTTGGGCCCAAAACCCCTAATGGGCCCTACGAATGCTGATTTAGCCCACTAAGCCTGCTTAA
1 GCTTTTGGGCCCAAAACCCCTAATGGGCCCTACGAATGCTGATTTAGCCCACTAAGCCTGCTTAA
*
600448 CCCAAATTTTACAACAATACTAACCGTGTTAACATGCAACTTTTCCAAATTCCATTTTCTATCAA
66 CCCAAATTTTACAACAATACTAACCGTGTTAACATGCAACTTTTCCAAATTCCATTTTATATCAA
600513 TTTTACCCAAATGGGCCCAAAAGCCCATTTGGCCCAAATTCCAGCCCATTGAGGCCCAACTTACC
131 TTTTACCCAAATGGGCCCAAAAGCCCATTTGGCCCAAATTCCAGCCCATTGAGGCCCAACTTACC
600578 ATCGTGCACAAAATTGAGTTCTTACCTGTTCCATCGATCCAAACACCGATCTTATCGTATTTATC
196 ATCGTGCACAAAATTGAGTTCTTACCTGTTCCATCGATCCAAACACCGATCTTATCGTATTTATC
600643 GTATCTATACCCATACGCAACATTACAAGTTCCCGAAATGCCGGTATTTTAGCATTTCGGCTTTT
261 GTATCTATACCCATACGCAACATTACAAGTTCCCGAAATGCCGGTATTTTAGCATTTCGGCTTTT
600708 CAGCAGATATTAATCTAAGCTACTACGAGGGTTAGTACACACCTGTTATGGGTTGAAGTTGAAAC
326 CAGCAGATATTAATCTAAGCTACTACGAGGGTTAGTACACACCTGTTATGGGTTGAAGTTGAAAC
600773 GTTTCCATAATCAATCACCTACGATAACCACCACCTGTCACTCAAACTTAACTAATCCAATATCA
391 GTTTCCATAATCAATCACCTACGATAACCACCACCTGTCACTCAAACTTAACTAATCCAATATCA
600838 ATATATGTAAATCCTAAGCACATCAGTCATACGGAACATAAGGGCATATTCGTCATTTTACCATA
456 ATATATGTAAATCCTAAGCACATCAGTCATACGGAACATAAGGGCATATTCGTCATTTTACCATA
*
600903 CAAGGGTATTACGGTCACTTTACCCTACAGGGGCTTTACGGTCTTTTTACCTATTAGGGGTATTT
521 CAAGGGTATTACGGTCACTTTACCCTACAGGGGCTTTACAGTCTTTTTACCTATTAGGGGTATTT
600968 TAGTCATTGCATCCTACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAGTTTTG
586 TAGTCATTGCATCCTACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAGTTTTG
601033 TAAACCAATGGTATTTCTATAATTTTTAAAAAGTCAATGGTATTTCTGTAATTTTATAAATTAAG
651 TAAACCAATGGTATTTCTATAATTTTTAAAAAGTCAATGGTATTTCTGTAATTTTATAAATTAAG
601098 GGTATTTTTGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTCGGT
716 GGTATTTTTGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTCGGT
601163 AATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCT
781 AATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCT
601228 ACA
846 ACA
601231 NNNNNGCTTTTGGGCCCAAAACCCCTAATGGGCCCTACGAATGCTGATTTAGCCCACTAAGCCTG
1 -----GCTTTTGGGCCCAAAACCCCTAATGGGCCCTACGAATGCTGATTTAGCCCACTAAGCCTG
*
601296 CTTAACCCAAATTTTACAATAATACTAACCGTGTTAACATGCAACTTTTCCAAATTCCATTTTAT
61 CTTAACCCAAATTTTACAACAATACTAACCGTGTTAACATGCAACTTTTCCAAATTCCATTTTAT
*
601361 ATCAATTTTACCCAAATGGGCCCAAAAGCCCATTTGGCCC-AATTCCTGCCCATTGAGGCCCAAC
126 ATCAATTTTACCCAAATGGGCCCAAAAGCCCATTTGGCCCAAATTCCAGCCCATTGAGGCCCAAC
601425 TTACCATCGTGCACAAAATTGAGTTCTTACCTGTTCCATCGATCCAAACACCGATCTTATCGTAT
191 TTACCATCGTGCACAAAATTGAGTTCTTACCTGTTCCATCGATCCAAACACCGATCTTATCGTAT
601490 TTATCGTATCTATACCCATACGCAACATTACAAGTTCCCGAAATGCCGGTATTTTAGCATTTCGG
256 TTATCGTATCTATACCCATACGCAACATTACAAGTTCCCGAAATGCCGGTATTTTAGCATTTCGG
601555 CTTTTCAGCAGATATTAATCTAAGCTACTACGAGGGTTAGTACACACCTGTTATGGGTTGAAGTT
321 CTTTTCAGCAGATATTAATCTAAGCTACTACGAGGGTTAGTACACACCTGTTATGGGTTGAAGTT
601620 GAAACGTTTCCATAATCAATCACCTACGATAACCACCACCTGTCACTCAAACTTAACTAATCCAA
386 GAAACGTTTCCATAATCAATCACCTACGATAACCACCACCTGTCACTCAAACTTAACTAATCCAA
601685 TATCAATATATGTAAATCCTAAGCACATCAGTCATACGGAACATAAGGGCATATTCGTCATTTTA
451 TATCAATATATGTAAATCCTAAGCACATCAGTCATACGGAACATAAGGGCATATTCGTCATTTTA
*
601750 CCATACAAGGGTATTACGGTCACTTTACCCTATAGGGGCTTTACAGTCTTTTTACCTATTAGGGG
516 CCATACAAGGGTATTACGGTCACTTTACCCTACAGGGGCTTTACAGTCTTTTTACCTATTAGGGG
601815 TATTTTAGTCATTGCATCCTACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAG
581 TATTTTAGTCATTGCATCCTACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAG
601880 TTTTGTAAACCAATGGTATTTCTATAATTTTTAAAAAGTCAATGGTATTTCTGTAATTTTATAAA
646 TTTTGTAAACCAATGGTATTTCTATAATTTTTAAAAAGTCAATGGTATTTCTGTAATTTTATAAA
601945 TTAAGGGTATTTTTGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATT
711 TTAAGGGTATTTTTGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATT
602010 TCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCT
776 TCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCT
602075 ATCCTACA
841 ATCCTACA
602083 G
1 G
602084 GGGTACTTCA
Statistics
Matches: 843, Mismatches: 5, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
847 1 0.00
852 679 0.81
853 163 0.19
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (848 bp):
GCTTTTGGGCCCAAAACCCCTAATGGGCCCTACGAATGCTGATTTAGCCCACTAAGCCTGCTTAA
CCCAAATTTTACAACAATACTAACCGTGTTAACATGCAACTTTTCCAAATTCCATTTTATATCAA
TTTTACCCAAATGGGCCCAAAAGCCCATTTGGCCCAAATTCCAGCCCATTGAGGCCCAACTTACC
ATCGTGCACAAAATTGAGTTCTTACCTGTTCCATCGATCCAAACACCGATCTTATCGTATTTATC
GTATCTATACCCATACGCAACATTACAAGTTCCCGAAATGCCGGTATTTTAGCATTTCGGCTTTT
CAGCAGATATTAATCTAAGCTACTACGAGGGTTAGTACACACCTGTTATGGGTTGAAGTTGAAAC
GTTTCCATAATCAATCACCTACGATAACCACCACCTGTCACTCAAACTTAACTAATCCAATATCA
ATATATGTAAATCCTAAGCACATCAGTCATACGGAACATAAGGGCATATTCGTCATTTTACCATA
CAAGGGTATTACGGTCACTTTACCCTACAGGGGCTTTACAGTCTTTTTACCTATTAGGGGTATTT
TAGTCATTGCATCCTACAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAATAGTTTTG
TAAACCAATGGTATTTCTATAATTTTTAAAAAGTCAATGGTATTTCTGTAATTTTATAAATTAAG
GGTATTTTTGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTCGGT
AATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCT
ACA
Found at i:602032 original size:81 final size:81
Alignment explanation
Indices: 601922--602072 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
601912 AAAAAGTCAA
* * * * *
601922 TGGTATTTCTGTAATTTTATAAATTAAGGGTATTTTTGTAATTTTACAAA-TTGAGGGTATTTCG
1 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTCG
601986 GTAATTTCACAAACTAG
65 GTAATTTCACAAACTAG
*
602003 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
1 TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGG
602068 TAATT
66 TAATT
602073 CTATCCTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 61 0.97
82 2 0.03
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (81 bp):
TGGTATTTCGGTAATTTTACAAACTAAGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTCGG
TAATTTCACAAACTAG
Found at i:602220 original size:81 final size:81
Alignment explanation
Indices: 602104--602301 Score: 281
Period size: 81 Copynumber: 2.4 Consensus size: 81
602094 GTAATTTCAC
* * * * *
602104 AATCGTGGGTAAAACGGTAATTTTGTAAA-CTAAGGGTAAAATGGTAATTTTGTAAATCGAAGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAATC-AAGGGTAAAATAGTAATTTTGTAAATCGAAGGT
* *
602168 AAAACGGTAATTTTGTA
65 AAAACGGTAATTCTATA
* *
602185 AATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATAGTAATTTTGTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATAGTAATTTTGTAAATCGAAGGTA
602250 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* *
602266 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATCAAGGG
602302 CATTTCAGTA
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 104 0.99
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATAGTAATTTTGTAAATCGAAGGTA
AAACGGTAATTCTATA
Found at i:602288 original size:27 final size:27
Alignment explanation
Indices: 602104--602301 Score: 236
Period size: 27 Copynumber: 7.3 Consensus size: 27
602094 GTAATTTCAC
* *
602104 AATCGTGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
*
602131 AA-CTAAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTGTA
* *
602158 AATCGAAGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
602185 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* *
602212 AATCAAGGGTAAAATAGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* * * *
602239 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTA
* **
602266 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTGTA
602293 AATCGAGGG
1 AATCGAGGG
602302 CATTTCAGTA
Statistics
Matches: 146, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 144 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTGTA
Found at i:613915 original size:757 final size:757
Alignment explanation
Indices: 612461--613974 Score: 2983
Period size: 757 Copynumber: 2.0 Consensus size: 757
612451 GCAACGCTGC
*
612461 TCAAATATCAGTGAGTTGAGGCAAAGCCTCCAGTACGTGGATAAACCACTTTCAATACTTCCTCC
1 TCAAATATCAGTAAGTTGAGGCAAAGCCTCCAGTACGTGGATAAACCACTTTCAATACTTCCTCC
612526 ATCAATACCCCAATCCCATGCAACATATATTAATAAAAGCATATCATGCAAAATACAGTATCAAT
66 ATCAATACCCCAATCCCATGCAACATATATTAATAAAAGCATATCATGCAAAATACAGTATCAAT
612591 CAGTCATGTAGTTTAGCCAATTTAAACCCTAGCGGTATTTCAGTAATTATGCTCTTTAGGGGTAG
131 CAGTCATGTAGTTTAGCCAATTTAAACCCTAGCGGTATTTCAGTAATTATGCTCTTTAGGGGTAG
612656 TTTCATAACTTACGCAACTACACAAGCTACTTCAGTAATTTTTAGCAATTTTATGCAATTTGGTT
196 TTTCATAACTTACGCAACTACACAAGCTACTTCAGTAATTTTTAGCAATTTTATGCAATTTGGTT
*
612721 CCACCATCTAACTAACAGGCTAATTTGCCCATATCTTACCCATATTGGTCCGTAAGCCCATTGTG
261 CCACCATCTAACTAACAGGCTAATTTGCCCATATCTTACCCATATTGGTCCGTAAGCCCATTGGG
612786 CCCAGTTTTGGCCCATCTGGCCCCTTTTTCCAAAGTACGCTAAAATGTCACACGAACTTACTTAC
326 CCCAGTTTTGGCCCATCTGGCCCCTTTTTCCAAAGTACGCTAAAATGTCACACGAACTTACTTAC
612851 CACTTTGTGGTGCTAGATCTAACAATTAATCTATGTCTTGAGAGCATTTGCATACTCACAAGCCT
391 CACTTTGTGGTGCTAGATCTAACAATTAATCTATGTCTTGAGAGCATTTGCATACTCACAAGCCT
612916 ATGAAATGCCGGAATTTCGGCATTTCGGCTTTTGTCGAATTGAACTAAGGAAGGGTGTTCAGTAC
456 ATGAAATGCCGGAATTTCGGCATTTCGGCTTTTGTCGAATTGAACTAAGGAAGGGTGTTCAGTAC
612981 ACACCTGATTCGTGATGACTGCTACTGAGATCTCTTACGATGTCCTACAATTGATTAGCACAGTT
521 ACACCTGATTCGTGATGACTGCTACTGAGATCTCTTACGATGTCCTACAATTGATTAGCACAGTT
613046 CTTATTTACAAACCATAATCACTAAACCCACAACCTACTTATCCATGACCGAACCATGTCCCTAA
586 CTTATTTACAAACCATAATCACTAAACCCACAACCTACTTATCCATGACCGAACCATGTCCCTAA
613111 AAGCCTTTGAAACCTTACCTTTTTGCCAAAATCGATAGCTAGCTCCGAATCCGATTGCTCCAACA
651 AAGCCTTTGAAACCTTACCTTTTTGCCAAAATCGATAGCTAGCTCCGAATCCGATTGCTCCAACA
613176 ACCCACGCCTTCAATCCAACACTTAAGAAGACACTAATCATT
716 ACCCACGCCTTCAATCCAACACTTAAGAAGACACTAATCATT
613218 TCAAATATCAGTAAGTTGAGGCAAAGCCTCCAGTACGTGGATAAACCACTTTCAATACTTCCTCC
1 TCAAATATCAGTAAGTTGAGGCAAAGCCTCCAGTACGTGGATAAACCACTTTCAATACTTCCTCC
613283 ATCAATACCCCAATCCCATGCAACATATATTAATAAAAGCATATCATGCAAAATACAGTATCAAT
66 ATCAATACCCCAATCCCATGCAACATATATTAATAAAAGCATATCATGCAAAATACAGTATCAAT
613348 CAGTCATGTAGTTTAGCCAATTTAAACCCTAGCGGTATTTCAGTAATTATGCTCTTTAGGGGTAG
131 CAGTCATGTAGTTTAGCCAATTTAAACCCTAGCGGTATTTCAGTAATTATGCTCTTTAGGGGTAG
* *
613413 TTTCATAACTTACGCAACTACACAAGCTACTTCAGTAATTTTTAGTAGTTTTATGCAATTTGGTT
196 TTTCATAACTTACGCAACTACACAAGCTACTTCAGTAATTTTTAGCAATTTTATGCAATTTGGTT
*
613478 CCACCATCTAACTAATAGGCTAATTTGCCCATATCTTACCCATATTGGTCCGTAAGCCCATTGGG
261 CCACCATCTAACTAACAGGCTAATTTGCCCATATCTTACCCATATTGGTCCGTAAGCCCATTGGG
613543 CCCAGTTTTGGCCCATCTGGCCCCTTTTTCCAAAGTACGCTAAAATGTCACACGAACTTACTTAC
326 CCCAGTTTTGGCCCATCTGGCCCCTTTTTCCAAAGTACGCTAAAATGTCACACGAACTTACTTAC
613608 CACTTTGTGGTGCTAGATCTAACAATTAATCTATGTCTTGAGAGCATTTGCATACTCACAAGCCT
391 CACTTTGTGGTGCTAGATCTAACAATTAATCTATGTCTTGAGAGCATTTGCATACTCACAAGCCT
613673 ATGAAATGCCGGAATTTCGGCATTTCGGCTTTTGTCGAATTGAACTAAGGAAGGGTGTTCAGTAC
456 ATGAAATGCCGGAATTTCGGCATTTCGGCTTTTGTCGAATTGAACTAAGGAAGGGTGTTCAGTAC
613738 ACACCTGATTCGTGATGACTGCTACTGAGATCTCTTACGATGTCCTACAATTGATTAGCACAGTT
521 ACACCTGATTCGTGATGACTGCTACTGAGATCTCTTACGATGTCCTACAATTGATTAGCACAGTT
613803 CTTATTTACAAACCATAATCACTAAACCCACAACCTACTTATCCATGACCGAACCATGTCCCTAA
586 CTTATTTACAAACCATAATCACTAAACCCACAACCTACTTATCCATGACCGAACCATGTCCCTAA
613868 AAGCCTTTGAAACCTTACCTTTTTGCCAAAATCGATAGCTAGCTCCGAATCCGATTGCTCCAACA
651 AAGCCTTTGAAACCTTACCTTTTTGCCAAAATCGATAGCTAGCTCCGAATCCGATTGCTCCAACA
613933 ACCCACGCCTTCAATCCAACACTTAAGAAGACACTAATCATT
716 ACCCACGCCTTCAATCCAACACTTAAGAAGACACTAATCATT
613975 GACAGAAACC
Statistics
Matches: 752, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
757 752 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (757 bp):
TCAAATATCAGTAAGTTGAGGCAAAGCCTCCAGTACGTGGATAAACCACTTTCAATACTTCCTCC
ATCAATACCCCAATCCCATGCAACATATATTAATAAAAGCATATCATGCAAAATACAGTATCAAT
CAGTCATGTAGTTTAGCCAATTTAAACCCTAGCGGTATTTCAGTAATTATGCTCTTTAGGGGTAG
TTTCATAACTTACGCAACTACACAAGCTACTTCAGTAATTTTTAGCAATTTTATGCAATTTGGTT
CCACCATCTAACTAACAGGCTAATTTGCCCATATCTTACCCATATTGGTCCGTAAGCCCATTGGG
CCCAGTTTTGGCCCATCTGGCCCCTTTTTCCAAAGTACGCTAAAATGTCACACGAACTTACTTAC
CACTTTGTGGTGCTAGATCTAACAATTAATCTATGTCTTGAGAGCATTTGCATACTCACAAGCCT
ATGAAATGCCGGAATTTCGGCATTTCGGCTTTTGTCGAATTGAACTAAGGAAGGGTGTTCAGTAC
ACACCTGATTCGTGATGACTGCTACTGAGATCTCTTACGATGTCCTACAATTGATTAGCACAGTT
CTTATTTACAAACCATAATCACTAAACCCACAACCTACTTATCCATGACCGAACCATGTCCCTAA
AAGCCTTTGAAACCTTACCTTTTTGCCAAAATCGATAGCTAGCTCCGAATCCGATTGCTCCAACA
ACCCACGCCTTCAATCCAACACTTAAGAAGACACTAATCATT
Found at i:626600 original size:43 final size:42
Alignment explanation
Indices: 626536--626635 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 42
626526 CATATCCTAG
* ** ** *
626536 ATATGGTCTTACATGGGATCTCATATTGATGCCAAAAGCCCAG
1 ATATGGTCTTACACGAAATCTCATACCGATGCC-AAAGCCCAA
* * *
626579 GTATGGTCTTACACGAAATCTCATACCGATGCCATATCCCAA
1 ATATGGTCTTACACGAAATCTCATACCGATGCCAAAGCCCAA
626621 ATATGGTCTTACACG
1 ATATGGTCTTACACG
626636 TAAACTCTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 20 0.43
43 27 0.57
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
ATATGGTCTTACACGAAATCTCATACCGATGCCAAAGCCCAA
Found at i:628318 original size:46 final size:45
Alignment explanation
Indices: 628268--628582 Score: 323
Period size: 46 Copynumber: 6.8 Consensus size: 45
628258 TGGTTAAGCA
*
628268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
628314 TCCGAACTCATTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
628361 TCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *** * *
628407 TCCGAACTCATTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
628454 TCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
628500 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
628546 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
628583 GTGGGTTACA
Statistics
Matches: 223, Mismatches: 32, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
43 2 0.01
44 6 0.03
45 2 0.01
46 143 0.64
47 60 0.27
48 2 0.01
49 6 0.03
50 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:628424 original size:93 final size:93
Alignment explanation
Indices: 628265--628528 Score: 474
Period size: 93 Copynumber: 2.8 Consensus size: 93
628255 GGATGGTTAA
* *
628265 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
628330 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
628358 GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
1 GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
628423 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * *
628451 GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
628516 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
628529 ACTTATGGAT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 165 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCCAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCATTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Done.